CHAPTER 1
DNA: The
Hereditary
Molecule
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Chapter 1 • Modern Genetics for All Students
What is the
Structure of
DNA?
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The Puzzle of DNA Structure
and Replication
INTRODUCTION
THE FUNCTION OF DNA is based entirely on its structure. A single strand of DNA consists of many individual building blocks called nucleotides that are connected, in a long
string, by chemical bonds. Each nucleotide contains one of four possible nitrogenous
bases: either adenine (A), cytosine (C), guanine (G), or thymine (T). In principle, it is
possible to construct a DNA strand that contains these four types of nucleotides in any
conceivable sequence. In nature, however, DNA exists as a double-stranded molecule in
which the two strands that lie side by side interact in a very specific way. The nature of the
interactions that occur between these two strands is such that the sequence of nitrogenous
bases on one strand always has a predictable relationship to the sequence of nitrogenous
bases on its partner strand. This relationship underlies the ability of DNA to serve as the
hereditary material and has sometimes been called “the fundamental secret of life.”
In this exercise, you will be provided with half of a file folder and a set of puzzle pieces of
different shapes and colors that represent the four kinds of nitrogenous bases that are found
in all DNA molecules. You will use these pieces to solve a simple puzzle, and from the finished puzzle, you should be able to figure out the nature of the relationship that exists
between opposite strands of a double-stranded DNA molecule, and why DNA is so easy to
replicate when a cell gets ready to divide.
MATERIALS
For each student or pair of students:
one half of a file folder
puzzle pieces
PROCEDURE, PART A
1. Draw a straight line near and parallel to the left
hand edge of your piece of file folder.
A
G
2. Select ten of your puzzle pieces at random, or in
any order that you wish. Place each of these
pieces on the paper so that it is letter-side-up and
so that its flat end touches the line you have
drawn (Fig. 1). This will be the left-hand strand
of your DNA puzzle.
Figure 1
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3. Now form the right-hand strand of the DNA by
placing the remaining puzzle pieces on the paper
so that the non-flat end each of them fits snugly
against the non-flat end of one of the pieces in the
left-hand strand.
A
G
T
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4. Draw a straight line next to the flat ends of the
pieces in the right hand strand (Fig. 2).
5. Use your finished puzzle to answer the first four
questions on the next page.
Figure 2
PROCEDURE, PART B
A
G
T
6. Pair up with another person in your class.
7. One person in each pair should put all of his or
her puzzle pieces back in the bag (Fig. 3).
Figure 3
8. Carefully transfer the right-hand strand of the
remaining DNA puzzle to the right hand side of
the other person’s piece of cardboard, leaving the
left-hand strand where it is (Fig. 4).
A
G
Figure 4
T
A
G
A
T
9. Use the puzzle pieces in the bag to build a second
DNA strand on each piece of cardboard (Fig. 5).
G
10. Answer questions 5 and 6 on the next page.
Figure 5
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Name __________________________________________________
Date ____________________________ Hour ________________
ANALYSIS AND CONCLUSIONS
1. Do you see any consistent relationship between the DNA bases (puzzle pieces) in one
strand of your puzzle and the bases with which they are paired in the other strand? If
so, state the nature of the relationship(s) you see.
______________________________________________________________________
______________________________________________________________________
2. Half of the puzzle pieces that you were given (the A’s and G’s) were much larger than
the other pieces (the C’s and T’s). Did this size difference cause your DNA model to be
significantly wider in some parts than in others? If not, why not?
______________________________________________________________________
______________________________________________________________________
3. Is there any consistent difference in the way that the pieces in the right-hand strands
and the left-hand strands of your model are oriented? If so, what is the difference?
______________________________________________________________________
______________________________________________________________________
4. How can you account for the fact that no matter which bases were selected for the lefthand strand of a DNA molecule, everyone had just the right pieces left over to assemble a matching right-hand strand?
______________________________________________________________________
______________________________________________________________________
Do Part B of the puzzle before you answer the next two questions.
5. Are the two DNA puzzles you now have the same or different? How can you account
for this?
______________________________________________________________________
______________________________________________________________________
6. What do you suppose biologists call this process of making two identical doublestranded DNA molecules from one when it occurs in cells?
______________________________________________________________________
______________________________________________________________________
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The Spiral Staircase
N 1944, A TEAM OF BIOLOGISTS LED BY OSWALD
AVERY MADE A VERY IMPORTANT DISCOVERY: DNA
EXTRACTED FROM ONE KIND OF BACTERIUM COULD BE
USED TO TRANSFER HERITABLE TRAITS OF THAT BACTERIUM TO A SECOND BACTERIUM! THIS WAS THE FIRST
CLEAR INDICATION THAT DNA WAS THE CARRIER OF
HEREDITARY INFORMATION. OTHER REPORTS DRAWING
THE SAME CONCLUSION SOON FOLLOWED.
I
BEFORE AVERY, SCIENTISTS HAD PAID LITTLE ATTENTION TO DNA. THEY KNEW IT CONTAINED THE SUGAR
DEOXYRIBOSE, PLENTY OF PHOSPHATE AND FOUR
BASES.
Reprinted with permission from Gonick, L. and Whellis, M. (1991).
The Cartoon Guide to Genetics. New York: Harper Collins
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What is a Model?
And What is it Good For?
AS WE GREW UP, most of us
played with various models:
model cars, model planes, model
houses (doll houses), model people (dolls), etc. Not all models are
designed for childhood play, however. Models serve important
functions in many areas of adult
life. Engineers, for example, evaluate various possible airplane
designs by building scale models
and examining how they behave
in a wind tunnel (which is itself a
model of the atmosphere).
Models are usually highly simplified relative to the objects that
they portray, and often several different models, simplified in different ways, are required
to study different aspects of the same object. For example, the engineer who is designing
the seats for a commercial airliner requires a very different kind of model than does the
engineer who is designing the wings. Neither of these models would necessarily be more
correct than the other; they would merely be simplified in different ways in order to serve
different purposes.
DNA MODELS
Scientists find models of various kinds of molecules very useful for visualizing how their
parts fit together and for predicting what their properties should be. Indeed, it was only
when two biologists by the names of Watson and Crick built the first fairly accurate scale
model of DNA that it became clear what the structure of real DNA molecules must be.
In the next exercise, you will build a much simpler DNA model than Watson and Crick did
in order to visualize certain very simple aspects of its structure. But as you progress in the
study of biology, you will probably encounter several other kinds of DNA models that are
constructed so as to reveal other, more detailed aspects of DNA structure and function.
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Building a Three-Dimensional
DNA Model
MATERIALS
For each student or pair of students: Use the following list to make sure that your modelbuilding kit contains the correct number of pieces of each type. Then use it to determine
what each of these pieces represents.
Short straws representing the nitrogenous bases:
3 blue straws
=
A (adenine)
3 red straws
=
T (thymine)
3 green straws
=
G (guanine)
3 gray straws
=
C (cytosine)
Pieces used to build the sugar-phosphate ladders:
12 black connectors =
sugars (deoxyribose)
12 red connectors
=
phosphate groups
24 yellow straws
=
sugar-to-phosphate bonds
6 white connectors =
hydrogen bonds
Pieces used to build the stand for the model:
1 long gray straw
3 medium-length green straws
1 four-prong black or silver connector
PROCEDURE
1. Make 12 nucleotides as shown in
figure 1. Each nucleotide will
require one deoxyribose sugar, two
yellow sugar-to-phosphate bonds,
one red phosphate group, and one
nitrogenous base (either red, green,
blue, or gray).
Phosphate
(red)
Deoxyribose (sugar)
(black)
Sugar-to-phosphate bonds
(yellow)
Nitrogen base
(blue, red, gray or green)
Figure 1: Making a nucleotide
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2. After you have made all the
nucleotides you can, use the
white connectors (hydrogen
bonds) to join them in pairs
according to the base-pairing rules (A to T and G to
C), as in figure 2.
Hydrogen bond
(white)
Figure 2: Making a nucleotide pair
3. After you have finished
forming the nucleotide
pairs, use the sugar-phosphate bonds to join them
(fig. 3), in any order you
want.
5’ end
3’ end
Deoxyribose sugar
(black)
Sugar-phosphate ladder
4. Note that the sugar-phosphate chain on the left side
has a red phosphate group
at the bottom (its 5’ end)
but not at the top (its 3’
end) and that the sugarphosphate chain on the right
side is just the opposite.
This is one of the ways that
enzymes that interact with
DNA molecules can tell the
two strands apart.
Hydrogen bond
(white)
Phosphate
(red)
Nitrogen base
(blue, red, gray or green)
Sugar-to-phosphate bonds
(yellow)
3’ end
5’ end
Figure 3: Joining the nucleotide pairs
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5. Build the stand for your
model using the one long
gray straw, the three medium-length green straws and
the four-pronged black connector.
6. Slide the white hydrogen
bonds that run down the
middle of your model onto
the stand.
7. To get all of your model to
fit on the stand, you will
need to twist it counterclockwise at the top (fig. 4).
Now you have a representation of the famous doublehelix of DNA.
8. Answer the questions on the
next page.
Figure 4: The completed model on a stand
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Name __________________________________________________
Date ____________________________ Hour ________________
ANALYSIS AND CONCLUSIONS
YOU HAVE NOW built two models of double-stranded DNA: the flat one in the puzzle at
the beginning of this exercise that you used to deduce the base-pairing rules and how DNA
is replicated (which we will call “model A”), and the one you have just built with straws
and connectors (which we will call “model B”). As mentioned earlier, often two models of
the same thing will be simplified in different ways to emphasize different features of the
object they are representing.
1. What feature or features of a double-stranded DNA molecule are represented better in
model A than in model B?
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
2. What feature or features of a double-stranded DNA molecule are represented better in
model B than in model A?
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
3. What feature or features of a double-stranded DNA molecule that you read about in the
excerpt from the Cartoon Guide to Genetics are not well represented in either model A
or model B?
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
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Date ____________________________ Hour ________________
DNA Model Questions
THE DIAGRAM ON THE left represents an
untwisted, double-stranded DNA molecule.
O
A
O
1. Label each sugar group on the diagram with
a letter S.
2. Label each phosphate group with a letter P.
O
O
3. One adenine (A) and one guanine (G) have
already been labeled. Label the rest of the
nitrogenous bases.
4. Circle one nucleotide. What three things go
together to make a nucleotide?
O
G
O
___________________________________
___________________________________
___________________________________
O
O
5. The sides of the DNA ladder are made up
of alternating ________________________
and ________________________ groups.
O
O
6. The rungs of the DNA ladder are made
up of _______________________________
7. A is always paired with ________________
O
O
8. G is always paired with ________________
9. Paired bases are held together by weak
bonds called __________________ bonds.
O
O
10. When the DNA ladder twists the way it
normally does, the shape of the molecule
is called a ___________________________
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Name __________________________________________________
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Date ____________________________ Hour ________________
DNA Word Search
FIND AND
CIRCLE the
words that go
with each of
the clues
given below.
Then write
the answers
on the lines
next to the
clues.
I
U
B
N
B
E
O
C
Z
H
T
Q
T
X
C
V
E
D
I
D
J Y R
S P G
E L D
S N P
A E I
B D A
S D B
U A W
O L W
N D V
E E N
G T A
O S D
R I S
T W B
I T I
N D X
E O Y
E J S
A X F
L
P
K
E
N
S
R
M
N
O
R
E
O
A
T
Y
B
E
E
M
W
Y
E
E
Y
Z
O
O
I
O
X
B
G
O
R
S
A
Y
A
N
X
J
Z
D
E
K
H
T
V
L
O
E
E
I
S
S
S
O
I
H
1. The nitrogenous base A ____________
B
W
P
Y
O
M
A
C
Y
D
S
L
B
W
D
T
E
W
E
G
V
L
H
W
X
C
K
J
N
C
C
O
J
N
G
G
P
X
Q
K
X M I U R W Y
S V Q E H B K
O S P H A T E
B L T T Q O U
I F C H X N C
R R Q L S I D
C P R M E P R
H I X L G O L
B N C N G V S
U U K E N E W
N Y N U N I S
F B Q I V E B
O E N I M Y H
P A L B S P D
U A H B J Z Z
M T S R A U H
A I R X Y Z O
I L E H E L B
V W Q X M L C
N X I
I A F R
T
D
L
A
Q
D
N
U
B
I
N
O
T
Q
Y
S
C
U
B
R
Q W D
N I
I
C T U
S H K
Y J R
G A T
G D I
L E S
F N L
S I Q
N N L
Q E I
B N X
Q N R
F O P
X A V
Y N Y
O D Q
X P V
G M Y
9. The name of the bonds that hold the
2. The nitrogenous base C ____________
two strands of DNA together (between
3. The nitrogenous base G ____________
the bases) ____________ (two words)
4. The nitrogenous base T ____________
5. The genetic material inside all cells
__________ (abbreviation)
6. The full name for DNA ____________
_______________________________
7 The scientific name for the shape of
the DNA molecule ________________
_______________________________
(two words)
8. The arrangement of two bases in the
DNA molecule forms a ____________
_____________________ (two words)
Chapter 1 • Modern Genetics for All Students
10. Pairs of these molecules form the steps
or rungs in the DNA molecule ______
_______________________________
(two words)
11. This subunit of DNA has three parts: a
phosphate, a sugar and a nitrogenous
base __________________________
12. The long backbones of the DNA molecule are made of alternating sugar and
__________________________ bonds.
13. This process occurs when DNA makes
a copy of itself ___________________
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